Where did "Open with" (user defined command) go?

I think you are looking for an answer like this. A user has asked for help on how to open fits file type that is not supported by default ubuntu programs.

IraGainesUK has posted the answer at http://ubuntuforums.org/showpost.php?p=12242314&postcount=5

I also can't believe it me took this long to figure out how to do such a simple thing in 12.04(!!), but the simple way is this:

1) Install Ubuntu Tweak:

sudo add-apt-repository ppa:tualatrix/ppa
sudo apt-get update
sudo apt-get install ubuntu-tweak

2) Open it up on the command line:

$ ubuntu-tweak

3) Navigate to Admins > File Type Manager and click All. This may take a moment whilst it scans all your mimetypes.

4) Uncheck Only show filetypes with associated applications at the bottom (again, may take some time).

5) Click anywhere in the right-hand panel and start typing fits to begin searching for the FITS document mimetype. Hopefully you should find it.

6) Double click it, and click Add and then your custom command (for me, topcat, for you, ds9).

I should note that I have tested the solution and it worked well for me.

If you right-click on any file and go to properties you'll find a dialog option to set the default application for opening such files.